Who needs hard drives? Store data in DNA!

One of the very first motion pictures ever made was of a galloping mare filmed in 1878 by the British photographer Eadweard Muybridge, who was trying to learn whether horses in motion ever become truly airborne. More than a century later, on 12 July 2017, Gina Kolata wrote in The New York Times that the clip is now the first movie ever to be encoded in the DNA of a living cell, where it can be retrieved at will and multiplied indefinitely as the host divides and grows. The advance is the latest and perhaps most astonishing example of the genome’s potential as a vast storage device.

Kolata wrote that scientists have already managed to translate all of Shakespeare’s sonnets into DNA. Dr. George Church, a geneticist at Harvard and one of the authors of the new study, recently encoded his own book, “Regenesis,” into bacterial DNA and made 90-billion copies of it.

With the new research, he and other scientists have begun to wonder if it may be possible to one day do something even stranger: to program bacteria to snuggle up to cells in the human body and to record what they are doing, in essence making a “movie” of each cell’s life.

On the left is an image of a human hand, which was encoded into nucleotides and captured by the CRISPR-Cas adaptation system in living bacteria. On the right is the image after multiple generations of bacterial growth, recovered by sequencing bacterial genomes. Image by Seth Shipman.

When a person gets ill, doctors might extract the bacteria and play back the record. It would be, said Dr. Church, analogous to the black boxes carried by airplanes whose data is used in the event of a crash.

At the moment all of this is “the other side of science fiction,” said Ewan Birney, director of the European Bioinformatics Institute and a member of the group that put Shakespeare’s sonnets in DNA.

Dr. Church and Dr. Seth Shipman, a geneticist, and their colleagues began by assigning each pixel in the black-and-white film a DNA code based on its shade of grey. The vast chains of DNA in each cell are made of just four molecules – adenine, guanine, thymine and cytosine – arranged in enormously varied configurations.

The geneticists ended up with a sequence of DNA molecules that represented the entirety of the film. Then they used a powerful new gene editing technique to slip this sequence into the genome of a common gut bacteria, E. coli. Despite the modification, the bacteria thrived and multiplied. The film stored in the genome was preserved intact with each new generation of progeny, the team found.

The renowned physicist Richard Feynman proposed half a century ago that DNA could be used for storage in this way. That was long before the molecular biology revolution, and decades before anyone could sequence DNA – much less edit it. Dr. Feynman’s idea “was an influential piece – it gave us a direction,” said Dr. Leonard Adleman, a mathematician at the University of Southern California and co-inventor of one of the most used public cryptography systems.

In 1994, Dr. Adleman reported that he had stored data in DNA and used it as a computer to solve a math problem. He determined that DNA can store a million times more data than a compact disc in the same space.

Data storage is a growing problem. Not only are significant amounts being generated, but the technology used to store it keeps becoming obsolete. DNA is never going out of fashion. Dr. Adleman noted that modern bacteria can read genes recovered from insects trapped in amber for millions of years.

For Dr. Shipman and Dr. Church, the immediate challenge is the brain. It contains 86-billion neurons, and there’s no easy way to know what they’re doing. “Right now, they can measure one neuron at a time with electrodes, but 86-billion electrodes would not fit in your brain. But gene-edited bacteria would “fit very nicely” according to the pair.

The idea is to have bacteria engineered as recording devices drift up to the brain in the blood and take notes for a while. Scientists would then extract the bacteria and examine their DNA to see what they had observed in the brain neurons.

Dr. Church and his colleagues have already shown in past research that bacteria can record DNA in cells, if the DNA is properly tagged. He gave as an example the sequencing of the human genome. The first effort took years and cost $3-billion. The wildest optimists predicted that in six decades each sequencing would cost $1000. It turned out it was six years, rather than six decades, says Dr. Church.

As digital information continues to accumulate, higher density and longer-term storage solutions are necessary. DNA has many potential advantages as a medium for immutable, high latency information storage needs. DNA’s essential biological role provides access to natural reading and writing enzymes and ensures that DNA will remain a readable standard for the foreseeable future.